CDO Singularity Support

Added by Kevin Manalo almost 7 years ago

Hello all,

I am not a CDO user, but I work to support the use of the tool on Johns Hopkins clusters for CDO users.

I would like to point out that we are using Singularity (singularity.lbl.gov) to support the use of CDO.

We have site-specific job scripts, but if there users out there using Singularity, I figured we should let you know that we are trying to maintain the Singularity file to keep up with CDO

https://github.com/marcc-hpc/cdo

The 'recipe' file is here:
https://github.com/marcc-hpc/cdo/blob/master/Singularity

This repo is used in conjunction with Singularity Hub
https://www.singularity-hub.org/collections
Keyword 'cdo'

Thanks!
Kevin

Replies (1)

RE: CDO Singularity Support - Added by Ralf Mueller almost 7 years ago

Hi Kevin!

Thx for maintaining another port for CDO and letting us know about it - never tried Singulariry myself. looks like a smarter way of using docker-like images, reminds me of conda.

regarding your recipe:

ECMWF has stopped developing grib_api. That's why we switched over to its followup eccodes. grib_api might be good for now, but I'm not sure, if updates to the GRIB2 standard tables will make it into it - so my recommondation is using eccodes as soon as possible.
there is no option --with-df5 in CDOs configure scripts (found it here: https://github.com/marcc-hpc/cdo/blob/master/Singularity#L54)
you can leave out =yes in all --with--xxxxxx options
for getting grib2 IO you need to provide the library to the CDO build system with --with-grib_api or --with-eccodes - atm your scripts seems to make independant builds of grib_api and cdo
for speed you might choose OpenMP parallelization by setting CXXFLAGS=-fopenmp and --with-fftw3 (eofs and filtering)
for automatic unity conversion with setpartab add --with-udunits2
for plotting, add --with-magics and --with-libxml2, but installaing magics++ is less funny than it sounds

hth
ralf

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